amplican
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see amplican.
Automated analysis of CRISPR experiments.
Bioconductor version: 3.6
`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.
Author: Kornel Labun [aut], Eivind Valen [cph, cre]
Maintainer: Eivind Valen <eivind.valen at gmail.com>
citation("amplican")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("amplican")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Alignment, CRISPR, Software, Technology, qPCR |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.4.0), methods, BiocGenerics(>= 0.22.0), Biostrings(>= 2.44.2), data.table (>= 1.10.4) |
| Imports | utils (>= 3.4.1), S4Vectors(>= 0.14.3), ShortRead(>= 1.34.0), IRanges(>= 2.10.2), GenomicRanges(>= 1.28.4), GenomeInfoDb(>= 1.12.2), BiocParallel(>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 2.2.0), ggbio(>= 1.24.1), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), clusterCrit (>= 1.2.7) |
| System Requirements | |
| URL | https://github.com/valenlab/amplican |
| Bug Reports | https://github.com/valenlab/amplican/issues |
See More
| Suggests | testthat, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | amplican_1.0.0.tar.gz |
| Windows Binary | amplican_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | amplican_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/amplican |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/amplican |
| Package Short Url | https://bioconductor.org/packages/amplican/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |